The film opens with text recapping the downfall of humanity after the spread of the virus that gave way to the rise of the apes led by Caesar. His funeral is shown, with his whole ape clan placing flowers on his head before his pyre is lit, and the apes honor their fallen leader.
Centuries later, apes have formed separate clans across the land. Three young apes – Noa (Owen Teague), Soona (Lydia Peckham), and Anaya (Travis Jeffery) – go out in search of eagle eggs for a bonding ritual since their clan trains eagles to help with tasks. After Soona and Anaya get their eggs, Noa climbs to the highest nest and manages to grab one before the mother eagle swipes at him and causes him to fall. Noa manages to catch himself on the side of an old building.
As the three start making their way down, Noa notices that his blanket is missing from his horse. They see a human outsider, known to the apes as “Echoes”, running around. The apes chase after the human, but she abandons the blanket and runs down a dark tunnel.
The three return to their village, where Noa’s father Koro (Neil Sandilands) is the chief, and they also live with his mother Dar (Sara Wiseman). Noa talks to Koro about the upcoming ritual for the next day but also warns him about going beyond the valley after catching the human’s scent on the blanket.
At night, Noa overhears a noise and finds the same human woman (Freya Allan) from earlier. She hits his chest and breaks the egg that he was keeping in his sack. While Soona and Anaya are willing to postpone their rituals alongside Noa’s, he refuses to let them do that and goes out for a replacement egg. He finds a deceased ape, along with one from his own clan coming to warn him after having a knife thrown in his back. Noa hides as a group of masked apes arrives. They find Noa’s horse and smack it so it can run back and lead them to the village.
When Noa returns, the entire village is on fire, and the masked apes are rounding up the members of Noa’s clan while yelling “For Caesar!”, including Dar, Soona, and Anaya. Noa goes to reach Koro, but he is found by a gorilla general named Sylva (Eka Darville). Koro’s eagle flies away, and Noa attempts to defend his father from Sylva. Koro fights back, but Sylva overpowers them both. He sends Noa falling from the tower before killing Koro.
In the morning, Noa finds himself alone amidst the ruins of his home. He walks until he finds Koro’s body and gives him a burial. He then sets forth to try and find his clan. Koro’s eagle reappears, but when Noa attempts to bond with it, the eagle claws his arm. He continues to travel and rests when necessary, but Noa ends up falling through a glass ceiling and into a trap. He cuts himself down but then is met by an orangutan named Raka (Peter Macon). He initially believes Noa is with the masked apes, but Noa explains his situation. Raka then says that he is burning the last ape of his clan before bringing Noa with him.
Raka explains that he is a follower of the real Caesar’s beliefs, belonging to a group called “The Order of Caesar” that he is now the only member of. The masked apes follow a tyrannical ape calling himself Proximus Caesar (Kevin Durand), who has taken the ways of Caesar and corrupted them to his benefit. Raka also tells Noa about when humans and apes co-existed alongside one another unlike now, and it is a belief Caesar held close.
Raka joins Noa in his mission to locate his clan, and on their way, they run into the young woman again after they set up camp. Raka gives her food and convinces Noa to give her his mother’s blanket for warmth, even though Noa does not trust her. Raka names her “Nova” after the human girl that Caesar befriended. Later at night, Caesar comes upon an observatory and looks up at the stars through a telescope. The woman then looks through the telescope and reacts with similar astonishment as Noa.
The following day, the woman joins Noa and Raka as they come upon a herd of zebra drinking from a lake. Suddenly, a group of humans emerge and also drink and bathe from the water. Then, Proximus’s apes arrive and start to round up the humans for sport. The woman hides in the grass while Raka tries to protect her, and Sylva goes hunting for her. Noa rides his horse to try and find both of them, but the woman yells out Noa’s name and is rescued by him. With Raka’s help, they outrun the villainous apes and make it to the shore. The woman then speaks and says her name is Mae, and she tells Noa that the apes are taking his clan to a bunker while she hopes to find other humans.
Continuing their travels, the three come across a bridge, but Sylva and his apes corner them. Mae falls into the river after another ape tries to grab her but gets swept away. Mae gets caught in a net as Raka tries to free her. He pulls her out but gets pulled down. When he tries to get back up, Sylva has Noa and Mae captured before he approaches the net with a knife. Raka reminds Noa of Caesar’s creed (“Apes together strong”) before Sylva cuts the net and sends Raka down the river.
Noa and Mae are taken to Proximus’s settlement, which is right next to a giant vault that he has been trying and failing to open for some time. Noa reunites with Dar, Soona, and Anaya before being taken with Mae to meet Proximus. He has been taught by another human, Trevathan (William H. Macy), who is willingly subservient to Proximus since he has accepted that humanity’s reign over Earth is long gone. Proximus explains that he plans to evolve and conquer once he learns the secrets of the vault, and he thinks Noa may be useful in his endeavors, while also warning him humans cannot be trusted. Outside, he speaks to Dar, who has come to accept her home is gone. Noa seems to have given up hope until he sees the necklace that Raka left him with, reminding him of Caesar’s ways and convincing himself that Proximus’s law is wrong.
Noa goes to find Mae and confront her over what it is she really wants. She tells him she is looking for something she says is like a book to help humans communicate again. They team up with Soona and Anaya to destroy what is inside the vault by getting it wet so that it may be useless to Proximus. Trevathan sees them and tells them their attempts will be futile. Mae tries to convince him to join them, but Trevathan has given up on humanity and is going to tell Proximus, so Mae chokes him to death and has the apes throw his body in the water. They then plant explosives around the dam and find their way through a secret entry that Mae knows about. Inside, the apes find picture books showing apes behind bars in zoos, while Mae finds her “book”, which is a deciphering key inside the vault’s machinery.
The heroes start to make their way out of the vault until they are met by Proximus and his apes. One of his lieutenants, Lightning (Ras-Samuel Weld A’abzgi), holds Soona at knifepoint as Proximus demands that Mae admit what her plan is. Mae takes out a gun she found in the fault and shoots Lightning in the chest, killing him. When Proximus asks if there are more guns, Mae says he cannot have what is inside and proceeds to blow the dam, flooding the bunker. Proximus’s apes are killed while the Eagle Clan starts climbing their way up. Noa is chased by Sylva, but he manages to squeeze his way through a gap that Sylva is too big for, leaving the brutish gorilla to drown.
The apes make their way up to the top, but Proximus finds them and begins to attack Noa for ruining his plans. He intends to make him bow before killing him, but Noa begins to chant his father’s songs to command the eagles, leading the rest of the clan to join him as the eagles proceed to attack Proximus, clawing and pecking at him until Dar has her eagle deal the final blow as the eagles pull Proximus over the ledge and send him plummeting to his watery grave.
Noa leads the apes back to their home, where they begin to rebuild. Mae finds them to come and bid Noa farewell, but he tells her he has come to agree with one thing that Proximus said, which is that humans will do anything to serve themselves. Mae admits that she is trying to get humans back to reclaiming their planet, but Noa questions where that will leave the apes.
Mae arrives at a human base and is met by a woman named Korina (Dichen Lachman). Mae gives her the deciphering key, which Korina brings to her team, and they use it to activate a network of satellites so that they may contact other human survivors. Meanwhile, Noa takes Soona to the observatory so she can look through the telescope up at the stars with him.
